1
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Song Y, Wu M, Wang C, Fang H, Lei X. Zn 2+ Binding Increases Parallel Structure in the Aβ(16-22) Oligomer by Disrupting Salt Bridge in Antiparallel Structure. J Phys Chem B 2024; 128:1385-1393. [PMID: 38294417 DOI: 10.1021/acs.jpcb.3c06925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The aggregation of monomeric amyloid β protein (Aβ) into oligomers and amyloid plaque in the brain is associated with Alzheimer's disease. The hydrophobic central core Aβ16-22 has been widely studied due to its essential role in the fibrillization of full-length Aβ peptides. Compared to the homogeneous antiparallel structure of Aβ16-22 at the late stage, the early-stage prefibrillar aggregates contain varying proportions of different β structures. In this work, we studied the appearance probabilities of various self-assembly structures of Aβ16-22 and the effects of Zn2+ on these probabilities by replica exchange molecular dynamics simulations. It was found that at room temperature, Aβ16-22 can readily form assembled β-sheet structures in pure water, where a typical antiparallel arrangement dominates (24.8% of all sampled trimer structures). The addition of Zn2+ to the Aβ16-22 solution will dramatically decrease the appearance probability of antiparallel trimer structures to 12.5% by disrupting the formation of the Lys16-Glu22 salt bridge. Meanwhile, the probabilities of hybrid antiparallel/parallel structures increase. Our simulation results not only reveal the competition between antiparallel and parallel structures in the Aβ16-22 oligomers but also show that Zn2+ can affect the oligomer structures. The results also provide insights into the role of metal ions in the self-assembly of short peptides.
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Affiliation(s)
- Yongshun Song
- School of Physics, East China University of Science and Technology, Shanghai 200237, China
| | - Mengjiao Wu
- School of Physics, East China University of Science and Technology, Shanghai 200237, China
| | - Changying Wang
- School of Sciences, Changzhou Institute of Technology, Changzhou 213032, China
| | - Haiping Fang
- School of Physics, East China University of Science and Technology, Shanghai 200237, China
- Department of Physics, Zhejiang Normal University, Jinhua 321004, China
| | - Xiaoling Lei
- School of Physics, East China University of Science and Technology, Shanghai 200237, China
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2
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Sementilli A, Rengifo RF, Li W, Stewart AM, Stewart KL, Twahir U, Kim Y, Yue J, Mehta AK, Shearer J, Warncke K, Lynn DG. Engineering Synthetic Electron Transfer Chains from Metallopeptide Membranes. Inorg Chem 2024; 63:2899-2908. [PMID: 38127051 PMCID: PMC10865380 DOI: 10.1021/acs.inorgchem.3c02861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
The energetic and geometric features enabling redox chemistry across the copper cupredoxin fold contain key components of electron transfer chains (ETC), which have been extended here by templating the cross-β bilayer assembly of a synthetic nonapeptide, HHQALVFFA-NH2 (K16A), with copper ions. Similar to ETC cupredoxin plastocyanin, these assemblies contain copper sites with blue-shifted (λmax 573 nm) electronic transitions and strongly oxidizing reduction potentials. Electron spin echo envelope modulation and X-ray absorption spectroscopies define square planar Cu(II) sites containing a single His ligand. Restrained molecular dynamics of the cross-β peptide bilayer architecture support metal ion coordination stabilizing the leaflet interface and indicate that the relatively high reduction potential is not simply the result of distorted coordination geometry (entasis). Cyclic voltammetry (CV) supports a charge-hopping mechanism across multiple copper centers placed 10-12 Å apart within the assembled peptide leaflet interface. This metal-templated scaffold accordingly captures the electron shuttle and cupredoxin functionality in a peptide membrane-localized electron transport chain.
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Affiliation(s)
- Anthony Sementilli
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Rolando F. Rengifo
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Wei Li
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Andrew M. Stewart
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Katie L. Stewart
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Umar Twahir
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Youngsun Kim
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Jipeng Yue
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Anil K. Mehta
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - Jason Shearer
- Department
of Chemistry, Trinity University, San Antonio, Texas 78212, United States
| | - Kurt Warncke
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
| | - David G. Lynn
- Departments
of Chemistry, Biology, and Physics, Emory University, Atlanta, Georgia 30322, United States
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3
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Klawa SJ, Lee M, Riker KD, Jian T, Wang Q, Gao Y, Daly ML, Bhonge S, Childers WS, Omosun TO, Mehta AK, Lynn DG, Freeman R. Uncovering supramolecular chirality codes for the design of tunable biomaterials. Nat Commun 2024; 15:788. [PMID: 38278785 PMCID: PMC10817930 DOI: 10.1038/s41467-024-45019-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/12/2024] [Indexed: 01/28/2024] Open
Abstract
In neurodegenerative diseases, polymorphism and supramolecular assembly of β-sheet amyloids are implicated in many different etiologies and may adopt either a left- or right-handed supramolecular chirality. Yet, the underlying principles of how sequence regulates supramolecular chirality remains unknown. Here, we characterize the sequence specificity of the central core of amyloid-β 42 and design derivatives which enable chirality inversion at biologically relevant temperatures. We further find that C-terminal modifications can tune the energy barrier of a left-to-right chiral inversion. Leveraging this design principle, we demonstrate how temperature-triggered chiral inversion of peptides hosting therapeutic payloads modulates the dosed release of an anticancer drug. These results suggest a generalizable approach for fine-tuning supramolecular chirality that can be applied in developing treatments to regulate amyloid morphology in neurodegeneration as well as in other disease states.
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Affiliation(s)
- Stephen J Klawa
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Michelle Lee
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Kyle D Riker
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Tengyue Jian
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
- Broad Pharm, San Diego, California, 92121, USA
| | - Qunzhao Wang
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Yuan Gao
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Margaret L Daly
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Shreeya Bhonge
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - W Seth Childers
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Tolulope O Omosun
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
- U.S. Department of Justice, Chicago, IL, 60603, USA
| | - Anil K Mehta
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
- The National High Magnetic Field Laboratory, University of Florida, Gainesville, FL, 32611, USA
| | - David G Lynn
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA.
- Department of Biology, Emory University, Atlanta, GA, 30322, USA.
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA.
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4
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Li F, Tang R, Kang Y, Cui X, Wang Y, Yang X. Fluorescent composite based on peptide nanotubes activating coumarin 6 for sensitive detection of new coccine in food samples. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 305:123492. [PMID: 37844452 DOI: 10.1016/j.saa.2023.123492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/18/2023] [Accepted: 10/02/2023] [Indexed: 10/18/2023]
Abstract
New coccine (NC), as a kind of common colorant, has been frequently used in our daily life. Herein, the fluorescent composite (PNTs@C6) prepared by the hydrophobic non-covalent interaction between peptide nanotubes and coumarin 6 (C6) was designed for the determination of NC. Due to the activation of C6 by peptide nanotubes, the composite exhibits strong green fluorescence emission, which can be selectively quenched by NC through the inner filter effect. Therefore, a new fluorescent method based on the PNTs@C6 composite for NC detection was constructed. Under optimal conditions, the fluorescence quenching of the sensor exhibits a good linear relationship with the concentration of NC in the range of 0.01-10 μM and the limit of detection is 3.6 nM. Furthermore, the strategy shows simplicity, rapid response and high selectivity and has been successfully applied to the detection of NC in food samples.
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Affiliation(s)
- Fang Li
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong 637000, China
| | - Rong Tang
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong 637000, China
| | - Yujie Kang
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong 637000, China
| | - Xiaoyan Cui
- Nanchong Food and Drug Inspection Institute, Nanchong 637000, China
| | - Ya Wang
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong 637000, China.
| | - Xiupei Yang
- College of Chemistry and Chemical Engineering, Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, China West Normal University, Nanchong 637000, China.
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5
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Nguyen PH, Derreumaux P. Multistep molecular mechanisms of Aβ16-22 fibril formation revealed by lattice Monte Carlo simulations. J Chem Phys 2023; 158:235101. [PMID: 37318171 DOI: 10.1063/5.0149419] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/26/2023] [Indexed: 06/16/2023] Open
Abstract
As a model of self-assembly from disordered monomers to fibrils, the amyloid-β fragment Aβ16-22 was subject to past numerous experimental and computational studies. Because dynamics information between milliseconds and seconds cannot be assessed by both studies, we lack a full understanding of its oligomerization. Lattice simulations are particularly well suited to capture pathways to fibrils. In this study, we explored the aggregation of 10 Aβ16-22 peptides using 65 lattice Monte Carlo simulations, each simulation consisting of 3 × 109 steps. Based on a total of 24 and 41 simulations that converge and do not converge to the fibril state, respectively, we are able to reveal the diversity of the pathways leading to fibril structure and the conformational traps slowing down the fibril formation.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, Université Paris Cité, UPR 9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- CNRS, Université Paris Cité, UPR 9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France (IUF), 75005 Paris, France
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6
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Kwak J, Woo J, Park S, Lim MH. Rational design of photoactivatable metal complexes to target and modulate amyloid-β peptides. J Inorg Biochem 2023; 238:112053. [PMID: 36347209 DOI: 10.1016/j.jinorgbio.2022.112053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/25/2022] [Accepted: 10/25/2022] [Indexed: 11/08/2022]
Abstract
The accumulation of amyloid-β (Aβ) aggregates is found in the brains of Alzheimer's disease patients. Thus, numerous efforts have been made to develop chemical reagents capable of targeting Aβ peptides and controlling their aggregation. In particular, tunable coordination and photophysical properties of transition metal complexes, with variable oxidation and spin states on the metal centers, can be utilized to probe Aβ aggregates and alter their aggregation profiles. In this review, we illustrate some rational strategies for designing photoactivatable metal complexes as chemical sensors for Aβ peptides or modulators against their aggregation pathways, with some examples.
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Affiliation(s)
- Jimin Kwak
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Junhyeok Woo
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Seongmin Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Mi Hee Lim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
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7
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Banerjee S, Baghel D, Iqbal MHU, Ghosh A. Nanoscale Infrared Spectroscopy Identifies Parallel to Antiparallel β-Sheet Transformation of Aβ Fibrils. J Phys Chem Lett 2022; 13:10522-10526. [PMID: 36342244 PMCID: PMC10079140 DOI: 10.1021/acs.jpclett.2c02998] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Spontaneous aggregation of amyloid beta (Aβ) proteins leading to the formation of oligomers and eventually into fibrils has been identified as a key pathological signature of Alzheimer's disease. The structure of late-stage aggregates have been studied in depth by conventional structural biology techniques, including nuclear magnetic resonance, X-ray crystallography, and infrared spectroscopy; however, the structure of early-stage aggregates is less known due to their transient nature. As a result, the structural evolution of amyloid aggregates from early oligomers to mature fibrils is still not fully understood. Here, we have applied atomic force microscopy-infrared nanospectroscopy to investigate the aggregation of Aβ 16-22, which spans the amyloidogenic core of the Aβ peptide. Our results demonstrate that Aβ 16-22 involves a structural transition from oligomers with parallel β-sheets to antiparallel fibrils through disordered and possibly helical intermediate fibril structures, contrary to the known aggregation pathway of full-length Aβ.
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Affiliation(s)
- Siddhartha Banerjee
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, AL 35487
| | - Divya Baghel
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, AL 35487
| | - Md Hasan ul Iqbal
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, AL 35487
| | - Ayanjeet Ghosh
- Department of Chemistry and Biochemistry, The University of Alabama, 1007E Shelby Hall, Tuscaloosa, AL 35487
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8
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Gordon-Kim C, Rha A, Poppitz GA, Smith-Carpenter J, Luu R, Roberson AB, Conklin R, Blake A, Lynn DG. Polyanion order controls liquid-to-solid phase transition in peptide/nucleic acid co-assembly. Front Mol Biosci 2022; 9:991728. [PMID: 36452451 PMCID: PMC9702359 DOI: 10.3389/fmolb.2022.991728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/25/2022] [Indexed: 01/06/2024] Open
Abstract
The Central Dogma highlights the mutualistic functions of protein and nucleic acid biopolymers, and this synergy appears prominently in the membraneless organelles widely distributed throughout prokaryotic and eukaryotic organisms alike. Ribonucleoprotein granules (RNPs), which are complex coacervates of RNA with proteins, are a prime example of these membranelles organelles and underly multiple essential cellular functions. Inspired by the highly dynamic character of these organelles and the recent studies that ATP both inhibits and templates phase separation of the fused in sarcoma (FUS) protein implicated in several neurodegenerative diseases, we explored the RNA templated ordering of a single motif of the Aβ peptide of Alzheimer's disease. We now know that this strong cross-β propensity motif alone assembles through a liquid-like coacervate phase that can be externally templated to form distinct supramolecular assemblies. Now we provide evidence that structured phosphates, ranging from complex structures like double stranded and quadraplex DNA to simple trimetaphosphate, differentially impact the liquid to solid phase transition necessary for paracrystalline assembly. The results from this simple model illustrate the potential of ordered environmental templates in the transition to potentially irreversible pathogenic assemblies and provides insight into the ordering dynamics necessary for creating functional synthetic polymer co-assemblies.
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Affiliation(s)
| | - Allisandra Rha
- Children’s Health of Orange County, Research Institute, Orange, CA, United States
| | - George A. Poppitz
- Department of Chemistry, Emory University, Atlanta, GA, United States
| | | | - Regina Luu
- Department of Chemistry, Emory University, Atlanta, GA, United States
| | | | - Russell Conklin
- Department of Chemistry, Emory University, Atlanta, GA, United States
| | - Alexis Blake
- Department of Chemistry, Emory University, Atlanta, GA, United States
| | - David G. Lynn
- Department of Chemistry, Emory University, Atlanta, GA, United States
- Department of Biology, Emory University, Atlanta, GA, United States
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9
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Yoshikawa Y, Yuzu K, Yamamoto N, Morishima K, Inoue R, Sugiyama M, Iwasaki T, So M, Goto Y, Tamura A, Chatani E. Pathway Dependence of the Formation and Development of Prefibrillar Aggregates in Insulin B Chain. Molecules 2022; 27:molecules27133964. [PMID: 35807211 PMCID: PMC9268647 DOI: 10.3390/molecules27133964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/18/2022] [Accepted: 06/19/2022] [Indexed: 11/16/2022] Open
Abstract
Amyloid fibrils have been an important subject as they are involved in the development of many amyloidoses and neurodegenerative diseases. The formation of amyloid fibrils is typically initiated by nucleation, whereas its exact mechanisms are largely unknown. With this situation, we have previously identified prefibrillar aggregates in the formation of insulin B chain amyloid fibrils, which have provided an insight into the mechanisms of protein assembly involved in nucleation. Here, we have investigated the formation of insulin B chain amyloid fibrils under different pH conditions to better understand amyloid nucleation mediated by prefibrillar aggregates. The B chain showed strong propensity to form amyloid fibrils over a wide pH range, and prefibrillar aggregates were formed under all examined conditions. In particular, different structures of amyloid fibrils were found at pH 5.2 and pH 8.7, making it possible to compare different pathways. Detailed investigations at pH 5.2 in comparison with those at pH 8.7 have suggested that the evolution of protofibril-like aggregates is a common mechanism. In addition, different processes of evolution of the prefibrillar aggregates have also been identified, suggesting that the nucleation processes diversify depending on the polymorphism of amyloid fibrils.
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Affiliation(s)
- Yuki Yoshikawa
- Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Hyogo, Japan; (Y.Y.); (K.Y.); (T.I.); (A.T.)
| | - Keisuke Yuzu
- Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Hyogo, Japan; (Y.Y.); (K.Y.); (T.I.); (A.T.)
| | - Naoki Yamamoto
- Division of Biophysics, Physiology, School of Medicine, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke 329-0498, Tochigi, Japan;
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2 Asashiro-Nishi, Kumatori, Sennan-gun 590-0494, Osaka, Japan; (K.M.); (R.I.); (M.S.)
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2 Asashiro-Nishi, Kumatori, Sennan-gun 590-0494, Osaka, Japan; (K.M.); (R.I.); (M.S.)
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2 Asashiro-Nishi, Kumatori, Sennan-gun 590-0494, Osaka, Japan; (K.M.); (R.I.); (M.S.)
| | - Tetsushi Iwasaki
- Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Hyogo, Japan; (Y.Y.); (K.Y.); (T.I.); (A.T.)
- Biosignal Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Hyogo, Japan
| | - Masatomo So
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Osaka, Japan;
| | - Yuji Goto
- Global Center for Medical Engineering and Informatics, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan;
| | - Atsuo Tamura
- Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Hyogo, Japan; (Y.Y.); (K.Y.); (T.I.); (A.T.)
| | - Eri Chatani
- Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Hyogo, Japan; (Y.Y.); (K.Y.); (T.I.); (A.T.)
- Correspondence:
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10
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Khurshid B, Rehman AU, Luo R, Khan A, Wadood A, Anwar J. Heparin-Assisted Amyloidogenesis Uncovered through Molecular Dynamics Simulations. ACS OMEGA 2022; 7:15132-15144. [PMID: 35572757 PMCID: PMC9089684 DOI: 10.1021/acsomega.2c01034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/11/2022] [Indexed: 05/14/2023]
Abstract
Glycosaminoglycans (GAGs), in particular, heparan sulfate and heparin, are found colocalized with Aβ amyloid. They have been shown to enhance fibril formation, suggesting a possible pathological connection. We have investigated heparin's assembly of the KLVFFA peptide fragment using molecular dynamics simulation, to gain a molecular-level mechanistic understanding of how GAGs enhance fibril formation. The simulations reveal an exquisite process wherein heparin accelerates peptide assembly by first "gathering" the peptide molecules and then assembling them. Heparin does not act as a mere template but is tightly coupled to the peptides, yielding a composite protofilament structure. The strong intermolecular interactions suggest composite formation to be a general feature of heparin's interaction with peptides. Heparin's chain flexibility is found to be essential to its fibril promotion activity, and the need for optimal heparin chain length and concentration has been rationalized. These insights yield design rules (flexibility; chain-length) and protocol guidance (heparin:peptide molar ratio) for developing effective heparin mimetics and other functional GAGs.
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Affiliation(s)
- Beenish Khurshid
- Department
of Biochemistry, Abdul Wali Khan University
Mardan, Mardan 23200, Pakistan
| | - Ashfaq Ur Rehman
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697, United States
| | - Ray Luo
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, California 92697, United States
| | - Alamzeb Khan
- Department
of Pediatrics, Yale School of Medicine, Yale University, New Haven, Connecticut 06511, United States
| | - Abdul Wadood
- Department
of Biochemistry, Abdul Wali Khan University
Mardan, Mardan 23200, Pakistan
| | - Jamshed Anwar
- Department
of Chemistry, University of Lancaster, Lancaster LA1 4YB, United Kingdom
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11
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Chatterjee A, Reja A, Pal S, Das D. Systems chemistry of peptide-assemblies for biochemical transformations. Chem Soc Rev 2022; 51:3047-3070. [PMID: 35316323 DOI: 10.1039/d1cs01178b] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
During the billions of years of the evolutionary journey, primitive polymers, involved in proto metabolic pathways with low catalytic activity, played critical roles in the emergence of modern enzymes with remarkable substrate specificity. The precise positioning of amino acid residues and the complex orchestrated interplay in the binding pockets of evolved enzymes promote covalent and non-covalent interactions to foster a diverse set of complex catalytic transformations. Recent efforts to emulate the structural and functional information of extant enzymes by minimal peptide based assemblies have attempted to provide a holistic approach that could help in discerning the prebiotic origins of catalytically active binding pockets of advanced proteins. In addition to the impressive sets of advanced biochemical transformations, catalytic promiscuity and cascade catalysis by such small molecule based dynamic systems can foreshadow the ancestral catalytic processes required for the onset of protometabolism. Looking beyond minimal systems that work close to equilibrium, catalytic systems and compartments under non-equilibrium conditions utilizing simple prebiotically relevant precursors have attempted to shed light on how bioenergetics played an essential role in chemical emergence of complex behaviour. Herein, we map out these recent works and progress where diverse sets of complex enzymatic transformations were demonstrated by utilizing minimal peptide based self-assembled systems. Further, we have attempted to cover the examples of peptide assemblies that could feature promiscuous activity and promote complex multistep cascade reaction networks. The review also covers a few recent examples of minimal transient catalytic assemblies under non-equilibrium conditions. This review attempts to provide a broad perspective for potentially programming functionality via rational selection of amino acid sequences leading towards minimal catalytic systems that resemble the traits of contemporary enzymes.
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Affiliation(s)
- Ayan Chatterjee
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Antara Reja
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Sumit Pal
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
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12
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Shen Y, Wang Y, Hamley IW, Qi W, Su R, He Z. Chiral self-assembly of peptides: Toward the design of supramolecular polymers with enhanced chemical and biological functions. Prog Polym Sci 2021. [DOI: 10.1016/j.progpolymsci.2021.101469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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13
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Oren O, Taube R, Papo N. Amyloid β structural polymorphism, associated toxicity and therapeutic strategies. Cell Mol Life Sci 2021; 78:7185-7198. [PMID: 34643743 PMCID: PMC11072899 DOI: 10.1007/s00018-021-03954-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/30/2021] [Accepted: 09/27/2021] [Indexed: 12/14/2022]
Abstract
A review of the multidisciplinary scientific literature reveals a large variety of amyloid-β (Aβ) oligomeric species, differing in molecular weight, conformation and morphology. These species, which may assemble via either on- or off-aggregation pathways, exhibit differences in stability, function and neurotoxicity, according to different experimental settings. The conformations of the different Aβ species are stabilized by intra- and inter-molecular hydrogen bonds and by electrostatic and hydrophobic interactions, all depending on the chemical and physical environment (e.g., solvent, ions, pH) and interactions with other molecules, such as lipids and proteins. This complexity and the lack of a complete understanding of the relationship between the different Aβ species and their toxicity is currently dictating the nature of the inhibitor (or inducer)-based approaches that are under development for interfering with (or inducing) the formation of specific species and Aβ oligomerization, and for interfering with the associated downstream neurotoxic effects. Here, we review the principles that underlie the involvement of different Aβ oligomeric species in neurodegeneration, both in vitro and in preclinical studies. In addition, we provide an overview of the existing inhibitors (or inducers) of Aβ oligomerization that serve as potential therapeutics for neurodegenerative diseases. The review, which covers the exciting studies that have been published in the past few years, comprises three main parts: 1) on- and off-fibrillar assembly mechanisms and Aβ structural polymorphism; 2) interactions of Aβ with other molecules and cell components that dictate the Aβ aggregation pathway; and 3) targeting the on-fibrillar Aβ assembly pathway as a therapeutic approach.
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Affiliation(s)
- Ofek Oren
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 84105, Beer-Sheva, Israel
- Department of Biotechnology Engineering, Avram and Stella Goldstein-Goren, National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O. Box 653, 84105, Beer-Sheva, Israel
| | - Ran Taube
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, P.O. Box 653, 84105, Beer-Sheva, Israel
| | - Niv Papo
- Department of Biotechnology Engineering, Avram and Stella Goldstein-Goren, National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O. Box 653, 84105, Beer-Sheva, Israel.
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14
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Misra S, Singh P, Mahata RN, Brandão P, Roy S, Mahapatra AK, Nanda J. Supramolecular Antiparallel β-Sheet Formation by Tetrapeptides Based on Amyloid Sequence. J Phys Chem B 2021; 125:4274-4285. [PMID: 33886330 DOI: 10.1021/acs.jpcb.0c10920] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Self-assembly of short peptides has emerged as an interesting research field for a wide range of applications. Recently, several truncated fragments of long-chain peptides or proteins responsible for different neurodegenerative diseases were studied to understand whether they can mimic the property and function of native peptides or not. It was reported that such a kind of peptide adopts a β-sheet structure in the disease state. It was observed that aromatic amino acid-rich peptide fragments possess a high tendency to adopt a β-sheet conformation. In this article, we are first time reporting the crystal structure of two tetrapeptides: Boc-GAII-OMe (Peptide 1) and Boc-GGVV-OMe (Peptide 2), composed of aliphatic amino acids, and the sequences are similar to the Aβ-peptide fragments Aβ29-32 and Aβ37-40 , respectively. In the solid-state, they are self-assembled in an antiparallel β-sheet fashion. The peptide units are connected by the strong amide hydrogen-bonding (N-H···O) interactions. Apart from that, other noncovalent interactions are also present, which help to stabilize the cross-β-sheet arrangement. Interestingly, in the crystal structure of Peptide 1, noncovalent C···C interaction between the electron-deficient carbonyl carbon, and the electron-rich sp3-carbon atom is observed, which is quite rare in the literature. The calculated torsion angles for these peptides are lying in the β-sheet region of the Ramachandran plot. FT-IR studies also indicate the formation of an antiparallel β-sheet structure in the solid-state. Circular dichroism of the peptides in the aqueous solution also suggests the presence of predominantly β-sheet-like conformation in the aqueous solution. Under cross-polarized light, Congo Red stained both peptides showed green-gold color due to birefringence indicating their amyloidogenic nature. This result indicates that the short peptide composed of aliphatic amino acid is capable of forming a β-sheet structure in the absence of aromatic amino acid and also can mimic the function of the native amyloid peptide.
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Affiliation(s)
- Souvik Misra
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, P.O.-Botanic Garden, Howrah-711103, West Bengal, India
| | - Pijush Singh
- Department of Biochemistry and Biophysics. University of Kalyani, Kalyani, Nadia, West Bengal, India
| | - Rabindra Nath Mahata
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, P.O.-Botanic Garden, Howrah-711103, West Bengal, India
| | - Paula Brandão
- Departamento de Química/CICECO, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Subhasish Roy
- Department of Chemistry, BITS-Pilani K. K. Birla Goa Campus, 433 Sancoale, Goa 403726, India
| | - Ajit K Mahapatra
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, P.O.-Botanic Garden, Howrah-711103, West Bengal, India
| | - Jayanta Nanda
- Department of Chemistry, University of North Bengal, Raja Rammohunpur, P.O.-NBU campus, Darjeeling-734013, West Bengal, India
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15
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Tan J, Zhang L, Hsieh MC, Goodwin JT, Grover MA, Lynn DG. Chemical control of peptide material phase transitions. Chem Sci 2021; 12:3025-3031. [PMID: 34164071 PMCID: PMC8179288 DOI: 10.1039/d0sc03666h] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Progressive solute-rich polymer phase transitions provide pathways for achieving ordered supramolecular assemblies. Intrinsically disordered protein domains specifically regulate information in biological networks via conformational ordering. Here we consider a molecular tagging strategy to control ordering transitions in polymeric materials and provide a proof-of-principle minimal peptide phase network captured with a dynamic chemical network. Substrate initiated assembly of a dynamic chemical network.![]()
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Affiliation(s)
- Junjun Tan
- Department of Chemistry and Biology, Emory University Atlanta Georgia 30322 USA
| | - Li Zhang
- Department of Chemistry and Biology, Emory University Atlanta Georgia 30322 USA
| | - Ming-Chien Hsieh
- Department of Chemistry and Biology, Emory University Atlanta Georgia 30322 USA .,School of Chemical and Biomolecular Engineering, Georgia Institute of Technology Atlanta Georgia 30332 USA
| | - Jay T Goodwin
- Department of Chemistry and Biology, Emory University Atlanta Georgia 30322 USA
| | - Martha A Grover
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology Atlanta Georgia 30332 USA
| | - David G Lynn
- Department of Chemistry and Biology, Emory University Atlanta Georgia 30322 USA
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16
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Gordon CK, Luu R, Lynn D. Capturing nested information from disordered peptide phases. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Regina Luu
- Departments of Chemistry and Biology Emory University Atlanta Georgia USA
| | - David Lynn
- Departments of Chemistry and Biology Emory University Atlanta Georgia USA
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17
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Liu S, Du P, Sun H, Yu HY, Wang ZG. Bioinspired Supramolecular Catalysts from Designed Self-Assembly of DNA or Peptides. ACS Catal 2020. [DOI: 10.1021/acscatal.0c03753] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Siyuan Liu
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
- College of Chemistry and Materials Science, Anhui Normal University, 189 Jiuhua Nanlu, Wuhu, Anhui 241002, China
| | - Peidong Du
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
| | - Hao Sun
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
| | - Hai-Yin Yu
- College of Chemistry and Materials Science, Anhui Normal University, 189 Jiuhua Nanlu, Wuhu, Anhui 241002, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic−Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing University of Chemical Technology, Beijing 100029, China
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18
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Haddad R, Ferraro E, Halmans A, Smith‐Carpenter JE. Modifying the surface of peptide nanofibers utilizing a thiol‐thioester exchange. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Ramiz Haddad
- Chemistry and Biochemistry Department Fairfield University Fairfield CT USA
| | - Elizabeth Ferraro
- Chemistry and Biochemistry Department Fairfield University Fairfield CT USA
| | - Ashley Halmans
- Chemistry and Biochemistry Department Fairfield University Fairfield CT USA
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19
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Amyloid assembly is dominated by misregistered kinetic traps on an unbiased energy landscape. Proc Natl Acad Sci U S A 2020; 117:10322-10328. [PMID: 32345723 DOI: 10.1073/pnas.1911153117] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Atomistic description of protein fibril formation has been elusive due to the complexity and long time scales of the conformational search. Here, we develop a multiscale approach combining numerous atomistic simulations in explicit solvent to construct Markov State Models (MSMs) of fibril growth. The search for the in-register fully bound fibril state is modeled as a random walk on a rugged two-dimensional energy landscape defined by β-sheet alignment and hydrogen-bonding states, whereas transitions involving states without hydrogen bonds are derived from kinetic clustering. The reversible association/dissociation of an incoming peptide and overall growth kinetics are then computed from MSM simulations. This approach is applied to derive a parameter-free, comprehensive description of fibril elongation of Aβ16-22 and how it is modulated by phenylalanine-to-cyclohexylalanine (CHA) mutations. The trajectories show an aggregation mechanism in which the peptide spends most of its time trapped in misregistered β-sheet states connected by weakly bound states twith short lifetimes. Our results recapitulate the experimental observation that mutants CHA19 and CHA1920 accelerate fibril elongation but have a relatively minor effect on the critical concentration for fibril growth. Importantly, the kinetic consequences of mutations arise from cumulative effects of perturbing the network of productive and nonproductive pathways of fibril growth. This is consistent with the expectation that nonfunctional states will not have evolved efficient folding pathways and, therefore, will require a random search of configuration space. This study highlights the importance of describing the complete energy landscape when studying the elongation mechanism and kinetics of protein fibrils.
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20
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Rengifo RF, Sementilli A, Kim Y, Liang C, Li NX, Mehta AK, Lynn DG. Liquid‐Like Phases Preorder Peptides for Supramolecular Assembly. CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.202000007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Rolando F. Rengifo
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - Anthony Sementilli
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - Youngsun Kim
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - Chen Liang
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - Noel Xiang'An Li
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - Anil K. Mehta
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
| | - David G. Lynn
- Chemistry Department Emory University 1515 Dickey Drive Atlanta GA 30322
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21
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Martial B, Raîche-Marcoux G, Lefèvre T, Audet P, Voyer N, Auger M. Structure of a Parkinson’s Disease-Involved α-Synuclein Peptide Is Modulated by Membrane Composition and Physical State. J Phys Chem B 2020; 124:3469-3481. [DOI: 10.1021/acs.jpcb.0c00945] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Benjamin Martial
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, 1045 avenue de la médecine, Québec, Quebec G1V 0A6, Canada
| | - Gabrielle Raîche-Marcoux
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, 1045 avenue de la médecine, Québec, Quebec G1V 0A6, Canada
| | - Thierry Lefèvre
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, 1045 avenue de la médecine, Québec, Quebec G1V 0A6, Canada
| | - Pierre Audet
- Department of Chemistry, Université Laval, 1045 avenue de la médecine, Québec, Quebec G1V 0A6, Canada
| | - Normand Voyer
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines (PROTEO), Université Laval, 1045 avenue de la médecine, Québec, Quebec G1V 0A6, Canada
| | - Michèle Auger
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, 1045 avenue de la médecine, Québec, Quebec G1V 0A6, Canada
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22
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Xing Y, Sun Y, Wang B, Ding F. Morphological Determinants of Carbon Nanomaterial-Induced Amyloid Peptide Self-Assembly. Front Chem 2020; 8:160. [PMID: 32211382 PMCID: PMC7076083 DOI: 10.3389/fchem.2020.00160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 02/24/2020] [Indexed: 01/12/2023] Open
Abstract
Hybridizing carbon nanomaterials (CNMs) with amyloid fibrils—the ordered nanostructures self-assembled by amyloidogenic peptides—has found promising applications in bionanotechology. Understanding fundamental interactions of CNMs with amyloid peptides and uncovering the determinants of their self-assembly structures and dynamics are, therefore, pivotal for enriching and enabling this novel class of hybrid nanomaterials. Here, we applied atomistic molecular dynamics simulations to investigate the self-assembly of two amyloid peptides—the amyloidogenic core residues 16-22 of amyloid-β (Aβ16−22) and the non-amyloid-β core of α-synuclein (NACore68−78)—on the surface of carbon nanotubes (CNT) with different sizes and chirality. Our computational results showed that with small radial CNTs, both types of peptides could form β-sheets wrapping around the nanotube surface into a supercoiled morphology. The angle between β-strands and nanotube axes in the supercoil structure depended mainly on the peptide sequence and CNT radius, but also weakly on the CNT chirality. Large radial CNTs and the extreme case of the flat graphene nanosheet, on the other hand, could nucleate amyloid fibrils perpendicular to the surface. Our results provided new insights of hybridizing CNMs with amyloid peptides and also offered a novel approach to manipulate the morphology of CNM-induced amyloid assembly by tuning the surface curvature, peptide sequence, and molecular ratio between peptides and available CNM surface area, which may be useful in engineering nanocomposites with high-order structures.
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Affiliation(s)
- Yanting Xing
- Department of Physics and Astronomy, Clemson University, Clemson, SC, United States
| | - Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC, United States
| | - Bo Wang
- Department of Physics and Astronomy, Clemson University, Clemson, SC, United States
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC, United States
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23
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Horváth D, Menyhárd DK, Perczel A. Protein Aggregation in a Nutshell: The Splendid Molecular Architecture of the Dreaded Amyloid Fibrils. Curr Protein Pept Sci 2020; 20:1077-1088. [PMID: 31553291 DOI: 10.2174/1389203720666190925102832] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 04/04/2019] [Accepted: 04/07/2019] [Indexed: 11/22/2022]
Abstract
The recent high-resolution structures of amyloid fibrils show that the organization of peptide segments into amyloid aggregate architecture is a general process, though the morphology is more complex and intricate than suspected previously. The amyloid fibrils are often cytotoxic, accumulating as intracellular inclusions or extracellular plaques and have the ability to interfere with cellular physiology causing various cellular malfunctions. At the same time, the highly ordered amyloid structures also present an opportunity for nature to store and protect peptide chains under extreme conditions - something that might be used for designing storage, formulation, and delivery of protein medications or for contriving bio-similar materials of great resistance or structure-ordering capacity. Here we summarize amyloid characteristics; discussing the basic morphologies, sequential requirements and 3D-structure that are required for the understanding of this newly (re)discovered protein structure - a prerequisite for developing either inhibitors or promoters of amyloid-forming processes.
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Affiliation(s)
- Dániel Horváth
- Laboratory of Structural Chemistry & Biology and MTA-ELTE Protein Modeling Research Group at the Institute of Chemistry, Eotvos Lorand University, H-1518, 112, PO Box 32, Budapest, Hungary
| | - Dóra K Menyhárd
- Laboratory of Structural Chemistry & Biology and MTA-ELTE Protein Modeling Research Group at the Institute of Chemistry, Eotvos Lorand University, H-1518, 112, PO Box 32, Budapest, Hungary
| | - András Perczel
- Laboratory of Structural Chemistry & Biology and MTA-ELTE Protein Modeling Research Group at the Institute of Chemistry, Eotvos Lorand University, H-1518, 112, PO Box 32, Budapest, Hungary
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24
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He Z, Li J, Chen SH, Zhou R. Surface Inhomogeneity of Graphene Oxide Influences Dissociation of Aβ 16-21 Peptide Assembly. J Phys Chem B 2019; 123:9098-9103. [PMID: 31566974 DOI: 10.1021/acs.jpcb.9b07359] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abnormal peptide assembly and aggregation is associated with an array of neurodegenerative diseases including Alzheimer's disease (AD). A detailed understanding of how nanostructured materials such as oxidized graphene perturb the peptide assembly and subsequently induce fibril dissociation may open new directions for the development of potential AD treatments. Here, we investigate the impact of surface inhomogeneity of graphene oxide (GO) on the assembly of amyloid-beta Aβ16-21 peptides on GO surfaces with different degrees of oxidation using molecular dynamics simulations. Interestingly, nonuniform GO nanosheets (in terms of oxidation sites) have a much stronger perturbation effect on the structure of Aβ16-21 assembly. The Aβ peptides exhibit a remarkable tendency in binding to the scattered interfaces between unoxidized and oxidized regions, which induces the dissociation of Aβ amyloid fibril. These findings should deepen our understanding of surface-induced peptide dissociation and stimulate discovery of alternative AD treatments.
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Affiliation(s)
| | | | - Serena H Chen
- Computational Biological Center , IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
| | - Ruhong Zhou
- Computational Biological Center , IBM Thomas J. Watson Research Center , Yorktown Heights , New York 10598 , United States
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25
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Ji W, Yuan C, Zilberzwige-Tal S, Xing R, Chakraborty P, Tao K, Gilead S, Yan X, Gazit E. Metal-Ion Modulated Structural Transformation of Amyloid-Like Dipeptide Supramolecular Self-Assembly. ACS NANO 2019; 13:7300-7309. [PMID: 31181152 DOI: 10.1021/acsnano.9b03444] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The misfolding of proteins and peptides potentially leads to a conformation transition from an α-helix or random coil to β-sheet-rich fibril structures, which are associated with various amyloid degenerative disorders. Inhibition of the β-sheet aggregate formation and control of the structural transition could therefore attenuate the development of amyloid-associated diseases. However, the structural transitions of proteins and peptides are extraordinarily complex processes that are still not fully understood and thus challenging to manipulate. To simplify this complexity, herein, the effect of metal ions on the inhibition of amyloid-like β-sheet dipeptide self-assembly is investigated. By changing the type and ratio of the metal ion/dipeptide mixture, structural transformation is achieved from a β-sheet to a superhelix or random coil, as confirmed by experimental results and computational studies. Furthermore, the obtained supramolecular metallogel exhibits excellent in vitro DNA binding and diffusion capability due to the positive charge of the metal/dipeptide complex. This work may facilitate the understanding of the role of metal ions in inhibiting amyloid formation and broaden the future applications of supramolecular metallogels in three-dimensional (3D) DNA biochip, cell culture, and drug delivery.
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Affiliation(s)
- Wei Ji
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv 6997801 , Israel
| | - Chengqian Yuan
- State Key Laboratory of Biochemical Engineering , Institute of Process Engineering, Chinese Academy of Sciences 100190 Beijing , China
| | - Shai Zilberzwige-Tal
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv 6997801 , Israel
| | - Ruirui Xing
- State Key Laboratory of Biochemical Engineering , Institute of Process Engineering, Chinese Academy of Sciences 100190 Beijing , China
| | - Priyadarshi Chakraborty
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv 6997801 , Israel
| | - Kai Tao
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv 6997801 , Israel
| | - Sharon Gilead
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv 6997801 , Israel
| | - Xuehai Yan
- State Key Laboratory of Biochemical Engineering , Institute of Process Engineering, Chinese Academy of Sciences 100190 Beijing , China
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences , Tel Aviv University , Tel Aviv 6997801 , Israel
- Department of Materials Science and Engineering Iby and Aladar Fleischman Faculty of Engineering Tel Aviv University , Tel Aviv 6997801 , Israel
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26
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Stoichiometry-controlled secondary structure transition of amyloid-derived supramolecular dipeptide co-assemblies. Commun Chem 2019. [DOI: 10.1038/s42004-019-0170-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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27
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Wakabayashi R, Suehiro A, Goto M, Kamiya N. Designer aromatic peptide amphiphiles for self-assembly and enzymatic display of proteins with morphology control. Chem Commun (Camb) 2019; 55:640-643. [PMID: 30628590 DOI: 10.1039/c8cc08163h] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We herein designed bi-functional aromatic peptide amphiphiles both self-assembling to fibrous nanomaterials and working as a substrate of microbial transglutaminase, leading to peptidyl scaffolds with different morphologies that can be enzymatically post-functionalized with proteins.
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Affiliation(s)
- Rie Wakabayashi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
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28
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Li X, Lei J, Qi R, Xie L, Wei G. Mechanistic insight into E22Q-mutation-induced antiparallel-to-parallel β-sheet transition of Aβ16−22fibrils: an all-atom simulation study. Phys Chem Chem Phys 2019; 21:15686-15694. [DOI: 10.1039/c9cp02561h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
E22Q mutation of Aβ16−22fibrils facilitates parallel β-sheet formation by enhancing Q22–Q22 hydrogen-bonding interaction and A21–A21, F20–F20, F19–F19 and V18–V18 hydrophobic interaction.
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Affiliation(s)
- Xuhua Li
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics
- Fudan University
- Shanghai
- China
| | - Jiangtao Lei
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics
- Fudan University
- Shanghai
- China
| | - Ruxi Qi
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics
- Fudan University
- Shanghai
- China
| | - Luogang Xie
- College of Physics and Electronic Engineering
- Zhengzhou University of Light Industry
- Zhengzhou 453002
- People's Republic of China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics
- Fudan University
- Shanghai
- China
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29
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Wilson CJ, Bommarius AS, Champion JA, Chernoff YO, Lynn DG, Paravastu AK, Liang C, Hsieh MC, Heemstra JM. Biomolecular Assemblies: Moving from Observation to Predictive Design. Chem Rev 2018; 118:11519-11574. [PMID: 30281290 PMCID: PMC6650774 DOI: 10.1021/acs.chemrev.8b00038] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Biomolecular assembly is a key driving force in nearly all life processes, providing structure, information storage, and communication within cells and at the whole organism level. These assembly processes rely on precise interactions between functional groups on nucleic acids, proteins, carbohydrates, and small molecules, and can be fine-tuned to span a range of time, length, and complexity scales. Recognizing the power of these motifs, researchers have sought to emulate and engineer biomolecular assemblies in the laboratory, with goals ranging from modulating cellular function to the creation of new polymeric materials. In most cases, engineering efforts are inspired or informed by understanding the structure and properties of naturally occurring assemblies, which has in turn fueled the development of predictive models that enable computational design of novel assemblies. This Review will focus on selected examples of protein assemblies, highlighting the story arc from initial discovery of an assembly, through initial engineering attempts, toward the ultimate goal of predictive design. The aim of this Review is to highlight areas where significant progress has been made, as well as to outline remaining challenges, as solving these challenges will be the key that unlocks the full power of biomolecules for advances in technology and medicine.
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Affiliation(s)
- Corey J. Wilson
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Andreas S. Bommarius
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Julie A. Champion
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yury O. Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Laboratory of Amyloid Biology & Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
| | - David G. Lynn
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Anant K. Paravastu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Chen Liang
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Ming-Chien Hsieh
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jennifer M. Heemstra
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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Li J, Zhan Z, Du X, Wang J, Hong B, Xu B. Selection of Secondary Structures of Heterotypic Supramolecular Peptide Assemblies by an Enzymatic Reaction. Angew Chem Int Ed Engl 2018; 57:11716-11721. [PMID: 29971927 PMCID: PMC6400471 DOI: 10.1002/anie.201806992] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Indexed: 01/28/2023]
Abstract
In a model study to investigate the consequence of reactions of intrinsically disordered regions (IDRs) of proteins in the context of the formation of highly ordered structures, we found that enzymatic reactions control the secondary structures of peptides during assembly. Specifically, phosphorylation of an α-helix-dominant peptide results in mostly disordered conformations, which become β-strand-dominant after enzymatic dephosphorylation to regenerate the peptide. In the presence of another peptide largely with a β-strand conformation, direct coassembly of the peptides results in amorphous aggregates consisting of α-helix and β-strand peptides, but the enzymatically generated peptide coassemblies (from the phosphopeptide) mainly adopt a β-strand conformation and form ordered structures (e.g., nanofibers). These results indicate that enzymatic dephosphorylation instructs conformationally flexible peptides to adopt thermodynamically favorable conformations in homotypic or heterotypic supramolecular assemblies.
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Affiliation(s)
- Jie Li
- Department of Chemistry, Brandeis University, 415 South St, Waltham, MA 02454 (USA),
| | - Ziqing Zhan
- Department of Chemistry, Brandeis University, 415 South St, Waltham, MA 02454 (USA),
| | - Xuewen Du
- Department of Chemistry, Brandeis University, 415 South St, Waltham, MA 02454 (USA),
| | - Jiaqing Wang
- Department of Chemistry, Brandeis University, 415 South St, Waltham, MA 02454 (USA),
| | - Brandon Hong
- Department of Chemistry, Brandeis University, 415 South St, Waltham, MA 02454 (USA),
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South St, Waltham, MA 02454 (USA),
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31
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Neves R, Stephens K, Smith-Carpenter JE. Synthesis and Characterization of 1,2-Dithiolane Modified Self-Assembling Peptides. J Vis Exp 2018:58135. [PMID: 30176010 PMCID: PMC6128216 DOI: 10.3791/58135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
This report focuses on the synthesis of an N-terminus 1,2-dithiolane modified self-assembling peptide and the characterization of the resulting self-assembled supramolecular structures. The synthetic route takes advantage of solid-phase peptide synthesis with the on-resin coupling of the dithiolane precursor molecule, 3-(acetylthio)-2-(acetylthiomethyl)propanoic acid, and the microwave-assisted thioacetate deprotection of the peptide N-terminus before final cleavage from the resin to yield the 1,2-dithiolane modified peptide. After the high-performance liquid chromatography (HPLC) purification of the 1,2-dithiolane peptide, derived from the nucleating core of the Aβ peptide associated with Alzheimer's disease, the peptide is shown to self-assemble into cross-β amyloid fibers. Protocols to characterize the amyloid fibers by Fourier-transform infrared spectroscopy (FT-IR), circular dichroism spectroscopy (CD) and transmission electron microscopy (TEM) are presented. The methods of N-terminal modification with a 1,2-dithiolane moiety to well-characterized self-assembling peptides can now be explored as model systems to develop post-assembly modification strategies and explore dynamic covalent chemistry on supramolecular peptide nanofiber surfaces.
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Affiliation(s)
- Ruben Neves
- Department of Chemistry and Biochemistry, Fairfield University
| | - Kailyn Stephens
- Department of Chemistry and Biochemistry, Fairfield University
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Harkness V RW, Avakyan N, Sleiman HF, Mittermaier AK. Mapping the energy landscapes of supramolecular assembly by thermal hysteresis. Nat Commun 2018; 9:3152. [PMID: 30089867 PMCID: PMC6082911 DOI: 10.1038/s41467-018-05502-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/02/2018] [Indexed: 01/28/2023] Open
Abstract
Understanding how biological macromolecules assemble into higher-order structures is critical to explaining their function in living organisms and engineered biomaterials. Transient, partly-structured intermediates are essential in many assembly processes and pathway selection, but are challenging to characterize. Here we present a simple thermal hysteresis method based on rapid, non-equilibrium melting and annealing measurements that maps the rate of supramolecular assembly as a function of temperature and concentration. A straightforward analysis of these surfaces provides detailed information on the natures of assembly pathways, offering temperature resolution beyond that accessible with conventional techniques. Validating the approach using a tetrameric guanine quadruplex, we obtain strikingly good agreement with previous kinetics measurements and reveal temperature-dependent changes to the assembly pathway. In an application to the recently discovered co-assembly of polydeoxyadenosine (poly(A)) and cyanuric acid, we show that fiber elongation is initiated when an unstable complex containing three poly(A) monomers acquires a fourth strand. Complex assembly pathways often involve transient, partly-formed intermediates that are challenging to characterize. Here, the authors present a simple and rapid spectroscopic thermal hysteresis method for mapping the energy landscapes of supramolecular assembly.
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Affiliation(s)
- Robert W Harkness V
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal Quebec, H3A 0B8, Canada
| | - Nicole Avakyan
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal Quebec, H3A 0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal Quebec, H3A 0B8, Canada
| | - Anthony K Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal Quebec, H3A 0B8, Canada.
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Bai Y, Chotera A, Taran O, Liang C, Ashkenasy G, Lynn DG. Achieving biopolymer synergy in systems chemistry. Chem Soc Rev 2018; 47:5444-5456. [PMID: 29850753 DOI: 10.1039/c8cs00174j] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Synthetic and materials chemistry initiatives have enabled the translation of the macromolecular functions of biology into synthetic frameworks. These explorations into alternative chemistries of life attempt to capture the versatile functionality and adaptability of biopolymers in new orthogonal scaffolds. Information storage and transfer, however, so beautifully represented in the central dogma of biology, require multiple components functioning synergistically. Over a single decade, the emerging field of systems chemistry has begun to catalyze the construction of mutualistic biopolymer networks, and this review begins with the foundational small-molecule-based dynamic chemical networks and peptide amyloid-based dynamic physical networks on which this effort builds. The approach both contextualizes the versatile approaches that have been developed to enrich chemical information in synthetic networks and highlights the properties of amyloids as potential alternative genetic elements. The successful integration of both chemical and physical networks through β-sheet assisted replication processes further informs the synergistic potential of these networks. Inspired by the cooperative synergies of nucleic acids and proteins in biology, synthetic nucleic-acid-peptide chimeras are now being explored to extend their informational content. With our growing range of synthetic capabilities, structural analyses, and simulation technologies, this foundation is radically extending the structural space that might cross the Darwinian threshold for the origins of life as well as creating an array of alternative systems capable of achieving the progressive growth of novel informational materials.
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Affiliation(s)
- Yushi Bai
- Emory University, 1521 Dickey Drive, Atlanta, Georgia 30322, USA.
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Li J, Zhan Z, Du X, Wang J, Hong B, Xu B. Selection of Secondary Structures of Heterotypic Supramolecular Peptide Assemblies by an Enzymatic Reaction. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806992] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jie Li
- Department of Chemistry Brandeis University 415 South Street Waltham MA 02454 USA
| | - Ziqing Zhan
- Department of Chemistry Brandeis University 415 South Street Waltham MA 02454 USA
| | - Xuewen Du
- Department of Chemistry Brandeis University 415 South Street Waltham MA 02454 USA
| | - Jiaqing Wang
- Department of Chemistry Brandeis University 415 South Street Waltham MA 02454 USA
| | - Brandon Hong
- Department of Chemistry Brandeis University 415 South Street Waltham MA 02454 USA
| | - Bing Xu
- Department of Chemistry Brandeis University 415 South Street Waltham MA 02454 USA
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35
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Liang C, Hsieh MC, Li NX, Lynn DG. Conformational evolution of polymorphic amyloid assemblies. Curr Opin Struct Biol 2018; 51:135-140. [DOI: 10.1016/j.sbi.2018.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/02/2018] [Accepted: 04/09/2018] [Indexed: 10/17/2022]
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36
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Nakagawa M, Kai S, Kojima T, Hiraoka S. Energy-Landscape-Independent Kinetic Trap of an Incomplete Cage in the Self-Assembly of a Pd 2 L 4 Cage. Chemistry 2018; 24:8804-8808. [PMID: 29683217 DOI: 10.1002/chem.201801183] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/20/2018] [Indexed: 01/16/2023]
Abstract
A kinetic trap is the metastable species that is transiently or constantly produced during the reaction by trapping in a deep energy well. In most cases, the reactivity of kinetically trapped species is relatively low under the reaction conditions. Herein, we report another type of kinetically trapped species that is an incomplete cage (IC) intermediate produced during the self-assembly of a Pd2 L4 cage from ditopic ligand (L) and PdII ions with a certain lifetime, although IC has a high enough reactivity to be converted into the cage with the reaction of free L, which was confirmed by the reaction of the isolated IC and L under the self-assembly conditions. IC was kinetically trapped not because IC lies on the bottom of a deep energy well but because the conversion of the intermediates essential for the conversion of IC to the cage preferentially takes place; IC was kinetically trapped independently of the shape of the energy landscape of the self-assembly.
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Affiliation(s)
- Masanori Nakagawa
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Shumpei Kai
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Tatsuo Kojima
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
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37
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Arnon ZA, Pinotsi D, Schmidt M, Gilead S, Guterman T, Sadhanala A, Ahmad S, Levin A, Walther P, Kaminski CF, Fändrich M, Schierle GSK, Adler-Abramovich L, Shimon LJW, Gazit E. Opal-like Multicolor Appearance of Self-Assembled Photonic Array. ACS APPLIED MATERIALS & INTERFACES 2018; 10:20783-20789. [PMID: 29842782 PMCID: PMC6358003 DOI: 10.1021/acsami.8b04912] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Molecular self-assembly of short peptide building blocks leads to the formation of various material architectures that may possess unique physical properties. Recent studies had confirmed the key role of biaromaticity in peptide self-assembly, with the diphenylalanine (FF) structural family as an archetypal model. Another significant direction in the molecular engineering of peptide building blocks is the use of fluorenylmethoxycarbonyl (Fmoc) modification, which promotes the assembly process and may result in nanostructures with distinctive features and macroscopic hydrogel with supramolecular features and nanoscale order. Here, we explored the self-assembly of the protected, noncoded fluorenylmethoxycarbonyl-β,β-diphenyl-Ala-OH (Fmoc-Dip) amino acid. This process results in the formation of elongated needle-like crystals with notable aromatic continuity. By altering the assembly conditions, arrays of spherical particles were formed that exhibit strong light scattering. These arrays display vivid coloration, strongly resembling the appearance of opal gemstones. However, unlike the Rayleigh scattering effect produced by the arrangement of opal, the described optical phenomenon is attributed to Mie scattering. Moreover, by controlling the solution evaporation rate, i.e., the assembly kinetics, we were able to manipulate the resulting coloration. This work demonstrates a bottom-up approach, utilizing self-assembly of a protected amino acid minimal building block, to create arrays of organic, light-scattering colorful surfaces.
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Affiliation(s)
- Zohar A. Arnon
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Dorothea Pinotsi
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | - Matthias Schmidt
- Institute of Protein Biochemistry, Ulm University, Ulm 89081, Germany
| | - Sharon Gilead
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tom Guterman
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Aditya Sadhanala
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Shahab Ahmad
- Institute for Manufacturing, Department of Engineering, University of Cambridge, Cambridge CB3 0FS, United Kingdom
| | - Aviad Levin
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, Ulm 89081, Germany
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, Ulm 89081, Germany
| | | | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Linda J. W. Shimon
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
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38
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Gobeaux F, Wien F. Reversible Assembly of a Drug Peptide into Amyloid Fibrils: A Dynamic Circular Dichroism Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:7180-7191. [PMID: 29772895 DOI: 10.1021/acs.langmuir.8b00094] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The common view on the amyloid fibril formation is that it is a multistep process that involves many oligomeric intermediate species, which leads to a high degree of polymorphism. This view derives from numerous kinetic studies whose vast majority was carried out with amyloid β fragments or other pathological amyloidogenic sequences. Yet, it is not clear whether the mechanisms inferred from these studies are universal and also apply to functional amyloids, in particular to peptide hormones which form reversible amyloid structures. In the present work, we study the self-assembly properties of atosiban, a nonapeptide drug, whose sequence is very close to those of the oxytocin and vasopressin hormones. We show that this very soluble peptide consistently self-assembles into 7 nm wide amyloid fibrils above a critical aggregation concentration (2-10 w/w % depending on the buffer conditions). The peptide system is characterized in details, from the monomeric to the assembled form, with osmotic concentration measurements, transmission electron microscopy, small-angle X-ray scattering, infrared and fluorescence spectroscopy, and circular dichroism (CD). We have followed in situ the fibril assembly with fluorescence and synchrotron radiation CD and noticed that the peptide undergoes conformational changes during the process. However, several lines of evidence point toward the association of monomers and dimers into fibrils without passing through oligomeric intermediate species contrary to what is usually reported for pathogenic amyloids. The native β-hairpin conformation of the monomer could explain the straightforward assembly. The tyrosine stacking is also shown to play an important role.
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Affiliation(s)
- Frédéric Gobeaux
- LIONS-NIMBE CEA, CNRS, Université Paris-Saclay, CEA Saclay , 91191 Gif-sur-Yvette Cedex , France
| | - Frank Wien
- SOLEIL Synchrotron , Saint Aubin 91190 , France
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39
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Dai C, Hao Y, Yu Y, Li M, Zhang SXA. Kinetic Study on the Self-Assembly of Au(I)-Thiolate Lamellar Sheets: Preassembled Precursor vs Molecular Precursor. J Phys Chem A 2018; 122:5089-5097. [PMID: 29800525 DOI: 10.1021/acs.jpca.8b02103] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular self-assembly has played an important role in nanofabrication. Due to the weak driving forces of noncovalent bonds, developing molecular nanoassemblies that have both robust preparation conditions and stable structure is a challenge. In our previous work, we have developed a reversible self-assembly system of Au(I)-thiolate coordination polymer (ATCP) to form colloidal lamellar sheets and demonstrated the high tailorability and stability of their structures, as well as their promising applications in gold nanocluster/nanoparticle fabrication and UV light shielding. Here, we first reported our progress in exploring a robust and green assembly protocol toward ATCP colloidal lamellar sheets in water by allowing the molecular precursors of HAuCl4 and the thiol ligand to form ATCP preassembled intermediates. In this way, colloidal ATCP lamellar sheets can be prepared in a wide range of synthetic concentrations ([Au]0 ≥ 2 × 10-4 M) and at broad assembly temperatures (80-100 °C) with similar high yields (>80%). The assembly kinetics at different conditions are also studied in detail to help understand the robust assembly process. The robust and green synthetic protocols will pave a way for their real applications.
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Affiliation(s)
- Chuying Dai
- State Key Lab of Supramolecular Structure and Materials, College of Chemistry , Jilin University , Changchun 130012 , P.R. China
| | - Yajiao Hao
- State Key Lab of Supramolecular Structure and Materials, College of Chemistry , Jilin University , Changchun 130012 , P.R. China
| | - Yang Yu
- State Key Lab of Supramolecular Structure and Materials, College of Chemistry , Jilin University , Changchun 130012 , P.R. China
| | - Minjie Li
- State Key Lab of Supramolecular Structure and Materials, College of Chemistry , Jilin University , Changchun 130012 , P.R. China
| | - Sean Xiao-An Zhang
- State Key Lab of Supramolecular Structure and Materials, College of Chemistry , Jilin University , Changchun 130012 , P.R. China
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40
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Zhang P, Cui Y, Anderson CF, Zhang C, Li Y, Wang R, Cui H. Peptide-based nanoprobes for molecular imaging and disease diagnostics. Chem Soc Rev 2018; 47:3490-3529. [PMID: 29497722 DOI: 10.1039/c7cs00793k] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Pathological changes in a diseased site are often accompanied by abnormal activities of various biomolecules in and around the involved cells. Identifying the location and expression levels of these biomolecules could enable early-stage diagnosis of the related disease, the design of an appropriate treatment strategy, and the accurate assessment of the treatment outcomes. Over the past two decades, a great diversity of peptide-based nanoprobes (PBNs) have been developed, aiming to improve the in vitro and in vivo performances of water-soluble molecular probes through engineering of their primary chemical structures as well as the physicochemical properties of their resultant assemblies. In this review, we introduce strategies and approaches adopted for the identification of functional peptides in the context of molecular imaging and disease diagnostics, and then focus our discussion on the design and construction of PBNs capable of navigating through physiological barriers for targeted delivery and improved specificity and sensitivity in recognizing target biomolecules. We highlight the biological and structural roles that low-molecular-weight peptides play in PBN design and provide our perspectives on the future development of PBNs for clinical translation.
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Affiliation(s)
- Pengcheng Zhang
- State Key Laboratory of Drug Research & Center for Pharmaceutics, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 501 Haike Road, Shanghai 201203, China.
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41
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Lee SJC, Nam E, Lee HJ, Savelieff MG, Lim MH. Towards an understanding of amyloid-β oligomers: characterization, toxicity mechanisms, and inhibitors. Chem Soc Rev 2018; 46:310-323. [PMID: 27878186 DOI: 10.1039/c6cs00731g] [Citation(s) in RCA: 335] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Alzheimer's disease (AD) is characterized by an imbalance between production and clearance of amyloid-β (Aβ) species. Aβ peptides can transform structurally from monomers into β-stranded fibrils via multiple oligomeric states. Among the various Aβ species, structured oligomers are proposed to be more toxic than fibrils; however, the identification of Aβ oligomers has been challenging due to their heterogeneous and metastable nature. Multiple techniques have recently helped us gain a better understanding of oligomers' assembly details and structural properties. Moreover, some progress on elucidating the mechanisms of oligomer-triggered toxicity has been made. Based on the collection of current findings, there is growing consensus that control of toxic Aβ oligomers could be a valid approach to regulate Aβ-associated toxicity, which could advance development of new diagnostics and therapeutics for amyloid-related diseases. In this review, we summarize the recent understanding of Aβ oligomers' assembly, structural properties, and toxicity, along with inhibitors against Aβ aggregation, including oligomerization.
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Affiliation(s)
- Shin Jung C Lee
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
| | - Eunju Nam
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
| | - Hyuck Jin Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Masha G Savelieff
- Department of Neurosurgery, University of Michigan, Ann Arbor 48109, MI, USA and SciGency Science Communications, Ann Arbor 48104, MI, USA
| | - Mi Hee Lim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
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42
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Lee MC, Yu WC, Shih YH, Chen CY, Guo ZH, Huang SJ, Chan JCC, Chen YR. Zinc ion rapidly induces toxic, off-pathway amyloid-β oligomers distinct from amyloid-β derived diffusible ligands in Alzheimer's disease. Sci Rep 2018; 8:4772. [PMID: 29555950 PMCID: PMC5859292 DOI: 10.1038/s41598-018-23122-x] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/06/2018] [Indexed: 11/15/2022] Open
Abstract
Alzheimer’s disease (AD) is the most prevalent neurodegenerative disease in the elderly. Zinc (Zn) ion interacts with the pathogenic hallmark, amyloid-β (Aβ), and is enriched in senile plaques in brain of AD patients. To understand Zn-chelated Aβ (ZnAβ) species, here we systematically characterized ZnAβ aggregates by incubating equimolar Aβ with Zn. We found ZnAβ40 and ZnAβ42 both form spherical oligomers with a diameter of ~12–14 nm composed of reduced β-sheet content. Oligomer assembly examined by analytical ultracentrifugation, hydrophobic exposure by BisANS spectra, and immunoreactivity of ZnAβ and Aβ derived diffusible ligands (ADDLs) are distinct. The site-specific 13C labeled solid-state NMR spectra showed that ZnAβ40 adopts β-sheet structure as in Aβ40 fibrils. Interestingly, removal of Zn by EDTA rapidly shifted the equilibrium back to fibrillization pathway with a faster kinetics. Moreover, ZnAβ oligomers have stronger toxicity than ADDLs by cell viability and cytotoxicity assays. The ex vivo study showed that ZnAβ oligomers potently inhibited hippocampal LTP in the wild-type C57BL/6JNarl mice. Finally, we demonstrated that ZnAβ oligomers stimulate hippocampal microglia activation in an acute Aβ-injected model. Overall, our study demonstrates that ZnAβ rapidly form toxic and distinct off-pathway oligomers. The finding provides a potential target for AD therapeutic development.
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Affiliation(s)
- Ming-Che Lee
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, R.O.C.,Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Wan-Cheng Yu
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | | | - Chun-Yu Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Zhong-Hong Guo
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Shing-Jong Huang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Jerry C C Chan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Yun-Ru Chen
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, R.O.C.. .,Genomics Research Center, Academia Sinica, Taipei, Taiwan.
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43
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Wang H, Feng Z, Del Signore SJ, Rodal AA, Xu B. Active Probes for Imaging Membrane Dynamics of Live Cells with High Spatial and Temporal Resolution over Extended Time Scales and Areas. J Am Chem Soc 2018; 140:3505-3509. [PMID: 29481071 PMCID: PMC5858877 DOI: 10.1021/jacs.7b13307] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Despite the advancement of molecular imaging techniques, there is an unmet need for probes for direct imaging of membrane dynamics of live cells. Here we report a novel type of active (or enzyme responsive) probes to directly image membrane dynamics of live cells with high spatial and temporal resolution over extended time scales and areas. Because lipid rafts enrich cholesterols and GPI-anchored enzymes (e.g., ectophosphatases), we design probes that consist of an enzymatic trigger, a fluorophore, and a cholesterol that are affinitive to the cell membrane. Being water-soluble and as the substrate of ectophosphatase, these cell compatible probes preferentially and rapidly assemble in plasma membrane, exhibit strong fluorescence, work at micromolar concentrations, and easily achieve high resolution monitoring of nanoscale heterogeneity in membranes of live cells, the release of exosomes, and the membrane dynamics of live cells. This work provides a facile means to link membrane dynamics and heterogeneity to cellular processes for understanding the interactions between membranes and proteins.
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Affiliation(s)
- Huaimin Wang
- Department of Chemistry , Brandeis University , 415 South Street , Waltham , Massachusetts 02453 , United States
| | - Zhaoqianqi Feng
- Department of Chemistry , Brandeis University , 415 South Street , Waltham , Massachusetts 02453 , United States
| | - Steven J Del Signore
- Department of Biology , Brandeis University , 415 South Street , Waltham , Massachusetts 02454 , United States
| | - Avital A Rodal
- Department of Biology , Brandeis University , 415 South Street , Waltham , Massachusetts 02454 , United States
| | - Bing Xu
- Department of Chemistry , Brandeis University , 415 South Street , Waltham , Massachusetts 02453 , United States
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44
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Tateishi T, Kojima T, Hiraoka S. Multiple Pathways in the Self-Assembly Process of a Pd 4L 8 Coordination Tetrahedron. Inorg Chem 2018; 57:2686-2694. [PMID: 29469572 DOI: 10.1021/acs.inorgchem.7b03085] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The self-assembly of a Pd418 coordination tetrahedron (Tet) from a ditopic ligand, 1, and palladium(II) ions, [PdPy*4]2+ (Py* = 3-chloropyridine), was investigated by a 1H NMR-based quantitative approach (quantitative analysis of self-assembly process, QASAP), which allows one to monitor the average composition of the intermediates not observed by NMR spectroscopy. The self-assembly of Tet takes place mainly through three pathways and about half of the Tet structures were produced through the reaction of a kinetically produced Pd3L6 double-walled triangle (DWT) and 200-nm-sized large intermediates (IntL). In two of the three pathways, the leaving ligand (Py*), which is not a component of Tet, catalytically assisted the self-assembly. Such a multiplicity of the self-assembly process of Tet suggests that molecular self-assembly takes place on an energy landscape like a protein-folding funnel.
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Affiliation(s)
- Tomoki Tateishi
- Department of Basic Science, Graduate School of Arts and Sciences , The University of Tokyo , 3-8-1 Komaba, Meguro-ku , Tokyo 153-8902 , Japan
| | - Tatsuo Kojima
- Department of Basic Science, Graduate School of Arts and Sciences , The University of Tokyo , 3-8-1 Komaba, Meguro-ku , Tokyo 153-8902 , Japan
| | - Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences , The University of Tokyo , 3-8-1 Komaba, Meguro-ku , Tokyo 153-8902 , Japan
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45
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Taran O, Chen C, Omosun TO, Hsieh MC, Rha A, Goodwin JT, Mehta AK, Grover MA, Lynn DG. Expanding the informational chemistries of life: peptide/RNA networks. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:rsta.2016.0356. [PMID: 29133453 DOI: 10.1098/rsta.2016.0356] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
The RNA world hypothesis simplifies the complex biopolymer networks underlining the informational and metabolic needs of living systems to a single biopolymer scaffold. This simplification requires abiotic reaction cascades for the construction of RNA, and this chemistry remains the subject of active research. Here, we explore a complementary approach involving the design of dynamic peptide networks capable of amplifying encoded chemical information and setting the stage for mutualistic associations with RNA. Peptide conformational networks are known to be capable of evolution in disease states and of co-opting metal ions, aromatic heterocycles and lipids to extend their emergent behaviours. The coexistence and association of dynamic peptide and RNA networks appear to have driven the emergence of higher-order informational systems in biology that are not available to either scaffold independently, and such mutualistic interdependence poses critical questions regarding the search for life across our Solar System and beyond.This article is part of the themed issue 'Reconceptualizing the origins of life'.
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Affiliation(s)
- Olga Taran
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Chenrui Chen
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Tolulope O Omosun
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Ming-Chien Hsieh
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Allisandra Rha
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Jay T Goodwin
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Anil K Mehta
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Martha A Grover
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - David G Lynn
- Department of Chemistry, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
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46
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Hsieh MC, Liang C, Mehta AK, Lynn DG, Grover MA. Multistep Conformation Selection in Amyloid Assembly. J Am Chem Soc 2017; 139:17007-17010. [PMID: 29111722 PMCID: PMC5709775 DOI: 10.1021/jacs.7b09362] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
![]()
Defining pathways
for amyloid assembly could impact therapeutic
strategies for as many as 50 disease states. Here we show that amyloid
assembly is subject to different forces regulating nucleation and
propagation steps and provide evidence that the more global β-sheet/β-sheet
facial complementarity is a critical determinant for amyloid nucleation
and structural selection.
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Affiliation(s)
- Ming-Chien Hsieh
- Georgia Institute of Technology , 311 Ferst Drive NW, Atlanta, Georgia 30332, United States
| | - Chen Liang
- Emory University , 1521 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Anil K Mehta
- Emory University , 1521 Dickey Drive, Atlanta, Georgia 30322, United States
| | - David G Lynn
- Emory University , 1521 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Martha A Grover
- Georgia Institute of Technology , 311 Ferst Drive NW, Atlanta, Georgia 30332, United States
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47
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van der Wel PCA. Insights into protein misfolding and aggregation enabled by solid-state NMR spectroscopy. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 88:1-14. [PMID: 29035839 PMCID: PMC5705391 DOI: 10.1016/j.ssnmr.2017.10.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/03/2017] [Accepted: 10/03/2017] [Indexed: 05/17/2023]
Abstract
The aggregation of proteins and peptides into a variety of insoluble, and often non-native, aggregated states plays a central role in many devastating diseases. Analogous processes undermine the efficacy of polypeptide-based biological pharmaceuticals, but are also being leveraged in the design of biologically inspired self-assembling materials. This Trends article surveys the essential contributions made by recent solid-state NMR (ssNMR) studies to our understanding of the structural features of polypeptide aggregates, and how such findings are informing our thinking about the molecular mechanisms of misfolding and aggregation. A central focus is on disease-related amyloid fibrils and oligomers involved in neurodegenerative diseases such as Alzheimer's, Parkinson's and Huntington's disease. SSNMR-enabled structural and dynamics-based findings are surveyed, along with a number of resulting emerging themes that appear common to different amyloidogenic proteins, such as their compact alternating short-β-strand/β-arc amyloid core architecture. Concepts, methods, future prospects and challenges are discussed.
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Affiliation(s)
- Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
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48
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Major Reaction Coordinates Linking Transient Amyloid-β Oligomers to Fibrils Measured at Atomic Level. Biophys J 2017; 113:805-816. [PMID: 28834717 DOI: 10.1016/j.bpj.2017.06.068] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/22/2017] [Accepted: 06/22/2017] [Indexed: 11/22/2022] Open
Abstract
The structural underpinnings for the higher toxicity of the oligomeric intermediates of amyloidogenic peptides, compared to the mature fibrils, remain unknown at present. The transient nature and heterogeneity of the oligomers make it difficult to follow their structure. Here, using vibrational and solid-state nuclear magnetic resonance spectroscopy, and molecular dynamics simulations, we show that freely aggregating Aβ40 oligomers in physiological solutions have an intramolecular antiparallel configuration that is distinct from the intermolecular parallel β-sheet structure observed in mature fibrils. The intramolecular hydrogen-bonding network flips nearly 90°, and the two β-strands of each monomeric unit move apart, to give rise to the well-known intermolecular in-register parallel β-sheet structure in the mature fibrils. Solid-state nuclear magnetic resonance distance measurements capture the interstrand separation within monomer units during the transition from the oligomer to the fibril form. We further find that the D23-K28 salt-bridge, a major feature of the Aβ40 fibrils and a focal point of mutations linked to early onset Alzheimer's disease, is not detectable in the small oligomers. Molecular dynamics simulations capture the correlation between changes in the D23-K28 distance and the flipping of the monomer secondary structure between antiparallel and parallel β-sheet architectures. Overall, we propose interstrand separation and salt-bridge formation as key reaction coordinates describing the structural transition of the small Aβ40 oligomers to fibrils.
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49
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Abstract
Living systems contain remarkable functional capability built within sophisticated self-organizing frameworks. Defining the assembly codes that coordinate these systems could greatly extend nanobiotechnology. To that end, we have highlighted the self-assembling architecture of the chlorosome antenna arrays and report the emulation and extension of their features for the development of cell-compatible photoredox materials. We specifically review work on amyloid peptide scaffolds able to (1) organize light-harvesting chromophores, (2) break peptide bilayer symmetry for directional energy and electron transfer, and (3) incorporate redox active metal ions at high density for energy storage.
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Affiliation(s)
- Rolando F Rengifo
- Emory University, Departments of Biology and Chemistry, 1515 Dickey Dr. NE, Atlanta, GA 30322, USA.
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50
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Patel S, Sasidhar YU, Chary KVR. Mechanism of Initiation, Association, and Formation of Amyloid Fibrils Modeled with the N-Terminal Peptide Fragment, IKYLEFIS, of Myoglobin G-Helix. J Phys Chem B 2017; 121:7536-7549. [PMID: 28707888 DOI: 10.1021/acs.jpcb.7b02205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Some peptides and proteins undergo self-aggregation under certain conditions, leading to amyloid fibrils formation, which is related to many disease conditions. It is important to understand such amyloid fibrils formation to provide mechanistic detail that governs the process. A predominantly α-helical myoglobin has been reported recently to readily form amyloid fibrils at a higher temperature, similar to its G-helix segment. Here, we have investigated the mechanism of amyloid fibrils formation by performing multiple long molecular dynamics simulations (27 μs) on the N-terminal segment of the G-helix of myoglobin. These simulations resulted in the formation of a single-layered tetrameric β-sheet with mixed parallel and antiparallel β-strands and this is the most common event irrespective of many different starting structures. Formation of the single-layered tetrameric β-sheet takes place following three distinctive pathways. The process of fibril initiation is dependent on temperature. Further, this study provides mechanistic insights into the formation of multilayered fibrilar structure, which could be applicable to a wider variety of peptides or proteins to understand the amyloidogenesis.
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Affiliation(s)
- Sunita Patel
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences , Hyderabad 500075, India.,UM-DAE Centre for Excellence in Basic Sciences , Mumbai University Campus, Mumbai 400098, India
| | - Yellamraju U Sasidhar
- Department of Chemistry, Indian Institute of Technology Bombay , Mumbai 400076, India
| | - Kandala V R Chary
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences , Hyderabad 500075, India.,Tata Institute of Fundamental Research , Mumbai 400005, India
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